Metadata-Version: 1.1
Name: fwdpy11
Version: 0.1.3a1
Summary: Forward-time population genetic simulation in Python
Home-page: http://molpopgen.github.io/fwdpy11
Author: Kevin Thornton
Author-email: krthornt@uci.edu
License: GPL >= 3
Description: fwdpy11
        *************************
        
        This is the README for fwdpy11_, which is a Python package for forward-time population genetic simulation.  It uses
        fwdpp_ as its C++ back-end.
        
        Build status
        -----------------------
        
        Master:
        
        .. image:: https://travis-ci.org/molpopgen/fwdpy11.svg?branch=master
            :target: https://travis-ci.org/molpopgen/fwdpy11
        
        Development: 
        
        .. image:: https://travis-ci.org/molpopgen/fwdpy11.svg?branch=dev
            :target: https://travis-ci.org/molpopgen/fwdpy11
        
        Manual
        -----------------------
        
        Latest/master:
        
        .. image:: https://readthedocs.org/projects/fwdpy11/badge/?version=latest
        	:target: http://fwdpy11.readthedocs.io/en/latest/?badge=latest
        
        Development branch:
        
        .. image:: https://readthedocs.org/projects/fwdpy11/badge/?version=dev
        	:target: http://fwdpy11.readthedocs.io/en/dev/?badge=dev
        
        Features
        -----------------------
        
        * Picklable population objects
        * Parallel computation via multiprocessing_ or concurrent.futures_.
        * Custom temporal samplers to analyze populations *during* a simulation may be written in pure Python.
          
        Dependencies
        -----------------------
        
        The following must be present on your system:
        
        * GSL_. This is a C library.  It is available via `conda`.
        * pybind11_. This should be installed via `pip` or `conda` as appropriate for your system.
        
        fwdpy11_ also uses fwdpp_, which is included as a submodule.
        
        License
        -----------------------
        
        GPLv3 or later (See COPYING)
        
        Suppored Python version
        -----------------------
        
        fwdpy11 is written for Python 3.  We will not modify the package to be compatible with Python 2.7.
        
        .. code-block:: bash
        
            git submodule init
            git submodule update
            python setup.py build_ext -i
            python test.py
        
        .. note::
            The clang compiler is the assumed default on OS X.  However, life is simpler
            if you use gcc.  The setup.py takes a --gcc option that eliminates OS X-specific
            (really Xcode clang-specific) features so that an OS X/gcc build is possible.
        
        Installation
        ---------------------------------
        
        Using pip on OS X and Linux (or pip3 as appropriate for your system):
        
        .. code-block:: bash
        
            pip install --upgrade fwdpy11
        
        If you prefer a pip install on OS X using GCC instead of clang:
        
        .. code-block:: bash
        
            pip install --upgrade fwdpy11 --install-option=--gcc
        
        You may or may not need to prefix the above with
        
        .. code-block:: bash
        
            CC=gcc CXX=g++
        
        depending on wheter or not your user's `$PATH` is set up to override Xcode's symlink of gcc to clang.
        
        Enabling assertions in the C++ code
        ------------------------------------------------------------------
        
        The C++ code uses C's assert macros in several places.  These are disabled by default.  However, it can be useful to
        enable them when hacking the code.  To do so:
        
        .. code-block:: bash
        
            python setup.py build_ext -i --debug
        
        .. note::
            Never install the package compiled in debug mode!  First, things will run much more slowly.  
            Second, triggering an assertion will cause the Python interpreter to crash.  These assertions
            exist as a brute-force method to help developers quickly identify bugs.
        
        Bioconda
        =================================
        
        fwdpy11 is available through bioconda_ for Linux and for OS X:
        
        .. code-block:: bash
        
            conda install -c bioconda fwdpy11
        
        The OS X build is built using gcc.
        
        .. _fwdpy11: http://molpopgen.github.io/fwdpy11
        .. _fwdpp: http://molpopgen.github.io/fwdpp
        .. _GSL: http://gnu.org/software/gsl
        .. _pybind11: https://github.com/pybind/pybind11
        .. _multiprocessing: https://docs.python.org/3/library/multiprocessing.html
        .. _concurrent.futures: https://docs.python.org/3/library/concurrent.futures.html
        .. _bioconda: https://bioconda.github.io/
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Requires: pybind11
Requires: numpy
Provides: fwdpy11
Obsoletes: none
